Markota, born in Sarajevo, fled Bosnia during the war and settled in Sweden, where he began to practice basketball. He played together with Maciej Lampe in Stockholm, until moving to Croatia when he was fourteen, after being invited to play in the Croatian league. Markota signed with KK Cibona, but was loaned to Zabok and Karlovac Šanac until the end of 2002–03. Subsequently, he received Croatian citizenship, declining an offer to play for the Swedish national basketball team. Markota was an early candidate for the 2004 NBA Draft, but soon withdrew his name from consideration. He was later invited to the Croatian national team, and in 2005 he changed his last name from "Omerhodžić" to "Markota". He was eventually chosen by the San Antonio Spurs in the second round of the 2006 NBA Draft, 59th overall, then immediately traded to the Milwaukee Bucks. During the summer of 2006, the Bucks signed Markota to a multi-year contract after the Spurs traded his draft rights for the higher of the Bucks’ two 2007 NBA draft second-round picks. In February 2007, the Bucks assigned Markota to Tulsa 66ers of the NBA Development League, in order to further improve his play. On September 7, Markota was waived by the Bucks, and signed with Russian team Spartak St. Petersburg on a two-year contract two days later. However, in early 2008, he switched to Lithuanian club Žalgiris Kaunas. On August 14, 2008, Markota was signed by Cibona, returning to the team he represented as a youngster but, after a series of unsatisfying performances upon recovering form knee injury, he was suspended for clashing with the coach. On October 28, 2008 ViveMenorca, of the Spanish ACB, announced the signing of Markota. In January 2009, he joined Iurbentia Bilbao. On September 1, 2010 he signed a one-year deal with Union Olimpija in Slovenia. In January 2012 he left Union Olimpija due to lack of payment and signed with KK Zagreb. He signed a contract with Beşiktaş in August 2012. On September 27, 2013, he signed a three-month contract with Brose Baskets. On November 25, 2013, he signed with his former club Bilbao Basket until the end of the season. In October 2014 Markota returns to Cibona for the third time signing a contact to last until the end of the season. On January 2, 2015 he parted ways with Cibona. The same day he signed with Turkish team İstanbul BB. On June 17, 2017, Markota signed with Turkish club Uşak Sportif. On December 4, 2017, he parted ways with Uşak, and signed with Croatian club Cedevita. In September 2018 Markota returned to Cibona for the third time in his career. In July 2019 Markota signed with the Montenegrin Mornar.
